Mercurial > repos > bebatut > qiime

annotate jackknifed_beta_diversity_through_plots_html_generation.py @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3
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4 import sys
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5 import os
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6 import argparse
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7 import re
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9
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10 def generate_index_html(dir_list, args):
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11 with open('index.html','w') as index_html_file:
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12 index_html_file.write('<html>\n')
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13 index_html_file.write('\t<head><title>Jackknifed beta diversity results</title></head>\n')
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14 index_html_file.write('\t<body>\n')
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15 index_html_file.write('\t\t<a href="http://www.qiime.org" target="_blank"><img src="http://qiime.org/_static/wordpressheader.png" alt="www.qiime.org""/></a>\n')
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16 index_html_file.write('\t\t<p>\n')
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17 index_html_file.write('\t\t\tBeta diversity metrics\n')
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18 index_html_file.write('\t\t\t<ul>\n')
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19
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20 for directory in dir_list:
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21 if directory == 'rarefaction':
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22 index_html_file.write('\t\t\t\t<li>' + directory)
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23 index_html_file.write('\t\t\t\t<ul>\n')
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24 for file_name in os.listdir(args.data_directory + '/' + directory):
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25 index_html_file.write('\t\t\t\t\t<li><a href="' + directory +
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26 '/' + file_name + '">' + file_name + '</a></li>\n')
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27 index_html_file.write('\t\t\t\t</ul>\n')
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28 index_html_file.write('\t\t\t\t</li>\n')
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29
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30 elif directory != 'unrarefied_bdiv':
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31 index_html_file.write('\t\t\t\t<li>' + directory)
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32 index_html_file.write('\t\t\t\t<ul>\n')
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34 index_html_file.write('\t\t\t\t\t<li>Rare distance matrix\n')
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35 index_html_file.write('\t\t\t\t\t<ul>\n')
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36 for file_name in os.listdir(args.data_directory + '/' + directory + '/rare_dm'):
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37 index_html_file.write('\t\t\t\t\t<li><a href="' + directory +
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38 '/rare_dm/' + file_name + '">' + file_name + '</a></li>\n')
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39 index_html_file.write('\t\t\t\t\t</ul>\n')
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40 index_html_file.write('\t\t\t\t\t</li>\n')
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41
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42 index_html_file.write('\t\t\t\t\t<li>Rare UPGMA tree\n')
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43 index_html_file.write('\t\t\t\t\t<ul>\n')
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44 for file_name in os.listdir(args.data_directory + '/' + directory + '/rare_upgma'):
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45 index_html_file.write('\t\t\t\t\t<li><a href="' + directory +
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46 '/rare_upgma/' + file_name + '">' + file_name + '</a></li>\n')
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47 index_html_file.write('\t\t\t\t\t</ul>\n')
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48 index_html_file.write('\t\t\t\t\t</li>\n')
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49
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50 index_html_file.write('\t\t\t\t\t<li>PCoA\n')
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51 index_html_file.write('\t\t\t\t\t<ul>\n')
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52 for file_name in os.listdir(args.data_directory + '/' + directory + '/pcoa'):
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53 index_html_file.write('\t\t\t\t\t<li><a href="' + directory +
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54 '/pcoa/' + file_name + '">' + file_name + '</a></li>\n')
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55 index_html_file.write('\t\t\t\t\t</ul>\n')
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56 index_html_file.write('\t\t\t\t\t</li>\n')
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57
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58 index_html_file.write('\t\t\t\t\t<li><a href="' + directory +
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59 '/emperor_pcoa_plots/index.html">PCoA plots</a></td></li>\n')
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61 index_html_file.write('\t\t\t\t</ul>\n')
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62 index_html_file.write('\t\t\t\t</li>\n')
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63
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64 index_html_file.write('\t\t\t</ul>\n')
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65 index_html_file.write('\t\t</p>\n')
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66 index_html_file.write('\t</body>\n')
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67 index_html_file.write('</html>\n')
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68
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69 def build_html(args):
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70 os.mkdir(args.html_dir)
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72 dir_list = [ name for name in os.listdir(args.data_directory) if
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73 os.path.isdir(os.path.join(args.data_directory, name)) ]
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74
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75 generate_index_html(dir_list, args)
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76
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77 os.system('cp -r index.html ' + args.html_dir)
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79 for directory in dir_list:
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80 os.system('cp -r ' + args.data_directory + '/' + directory + ' ' +
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81 args.html_dir)
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82
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83 os.system('mv ' + args.html_dir + '/index.html ' + args.html_file)
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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84
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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85 if __name__ == '__main__':
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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86 parser = argparse.ArgumentParser()
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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87 parser.add_argument('--data_directory', required=True)
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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88 parser.add_argument('--html_file', required=True)
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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89 parser.add_argument('--html_dir', required=True)
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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90 args = parser.parse_args()
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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91
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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92 build_html(args)